Variant report

Variant	rs375883
Chromosome Location	chr6:167384714-167384715
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:167376063..167378279-chr6:167383576..167385467,2	K562	blood:
2	chr6:167382648..167385296-chr6:167441304..167444220,2	K562	blood:
3	chr6:167383062..167385710-chr6:167390180..167391984,2	MCF-7	breast:
4	chr6:167368947..167370452-chr6:167382818..167385059,2	K562	blood:
5	chr6:167372022..167374249-chr6:167383520..167385172,2	K562	blood:
6	chr6:167383885..167385840-chr6:167392702..167394703,2	K562	blood:

Variant related genes	Relation type
ENSG00000249141	Chromatin interaction
ENSG00000026297	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs12193528	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12212326	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs150116	0.83[AMR][1000 genomes]
rs151604	0.85[MEX][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes]
rs16899770	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16899771	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16899777	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16899781	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16899788	0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16899799	0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16899801	0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16899809	0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16899811	1.00[JPT][hapmap]
rs16899812	1.00[JPT][hapmap]
rs16899821	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs16899825	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs16899828	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs16899831	1.00[JPT][hapmap]
rs16899833	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs17856382	0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1794698	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2273746	0.85[JPT][hapmap]
rs239932	0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34585172	0.81[ASN][1000 genomes]
rs3798305	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs3798308	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3798309	1.00[JPT][hapmap]
rs3798310	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3798311	0.81[ASN][1000 genomes]
rs3798312	0.81[ASN][1000 genomes]
rs3798313	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3822914	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs388036	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269603	0.81[ASN][1000 genomes]
rs41269605	0.81[ASN][1000 genomes]
rs414431	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs417607	0.94[AMR][1000 genomes]
rs425145	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435359	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435688	0.82[LWK][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs443297	0.91[AMR][1000 genomes]
rs56028052	0.81[ASN][1000 genomes]
rs56266102	0.90[ASN][1000 genomes]
rs61751042	0.81[ASN][1000 genomes]
rs6905912	0.90[ASN][1000 genomes]
rs6907391	0.90[ASN][1000 genomes]
rs6907735	0.90[ASN][1000 genomes]
rs6922071	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs73024229	1.00[ASN][1000 genomes]
rs73024302	0.90[ASN][1000 genomes]
rs73026203	0.81[ASN][1000 genomes]
rs73026206	0.81[ASN][1000 genomes]
rs73026210	0.81[ASN][1000 genomes]
rs73026212	0.81[ASN][1000 genomes]
rs73026214	0.81[ASN][1000 genomes]
rs73026216	0.81[ASN][1000 genomes]
rs73026224	0.81[ASN][1000 genomes]
rs73026225	0.81[ASN][1000 genomes]
rs73026226	0.81[ASN][1000 genomes]
rs73026230	0.81[ASN][1000 genomes]
rs73026236	0.81[ASN][1000 genomes]
rs73026238	0.81[ASN][1000 genomes]
rs73026240	0.81[ASN][1000 genomes]
rs73026241	0.81[ASN][1000 genomes]
rs73026247	0.81[ASN][1000 genomes]
rs73026249	0.81[ASN][1000 genomes]
rs73026251	0.81[ASN][1000 genomes]
rs73028276	0.81[ASN][1000 genomes]
rs73028277	0.81[ASN][1000 genomes]
rs73028278	0.81[ASN][1000 genomes]
rs73028283	0.81[ASN][1000 genomes]
rs73028285	0.81[ASN][1000 genomes]
rs73028286	0.81[ASN][1000 genomes]
rs73028287	0.81[ASN][1000 genomes]
rs73028288	0.81[ASN][1000 genomes]
rs73028290	0.81[ASN][1000 genomes]
rs73028292	0.81[ASN][1000 genomes]
rs73028293	0.81[ASN][1000 genomes]
rs73028295	0.81[ASN][1000 genomes]
rs73028297	0.81[ASN][1000 genomes]
rs73028298	0.81[ASN][1000 genomes]
rs73028301	0.81[ASN][1000 genomes]
rs73030105	0.81[ASN][1000 genomes]
rs73030106	0.81[ASN][1000 genomes]
rs73030108	0.81[ASN][1000 genomes]
rs73030112	0.81[ASN][1000 genomes]
rs73041500	0.91[ASN][1000 genomes]
rs73043118	1.00[ASN][1000 genomes]
rs73043122	1.00[ASN][1000 genomes]
rs73043163	1.00[ASN][1000 genomes]
rs7744664	0.90[ASN][1000 genomes]
rs9459809	0.80[YRI][hapmap]
rs9459815	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1034359	chr6:167359643-167384714	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs375883	RNASET2	Cis_1M	lymphoblastoid	RTeQTL
rs375883	CCR6	cis	cerebellum	SCAN
rs375883	PHF10	cis	parietal	SCAN
rs375883	FGFR1OP	cis	lymphoblastoid	seeQTL
rs375883	RNASET2	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167371400-167411000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:167373600-167402400	Weak transcription	Liver	Liver
3	chr6:167373800-167384800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:167378800-167398600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:167380800-167391000	Weak transcription	Osteobl	bone
6	chr6:167381200-167410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:167381200-167411000	Weak transcription	Fetal Stomach	stomach
8	chr6:167381600-167385200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr6:167381800-167391200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:167381800-167396200	Weak transcription	HepG2	liver
11	chr6:167382000-167411200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:167382200-167385400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr6:167382400-167392400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:167382400-167402200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:167382600-167384800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:167382600-167385200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:167382600-167385400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:167382600-167392000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:167382800-167385000	Enhancers	Fetal Thymus	thymus
20	chr6:167383000-167385000	Enhancers	Thymus	Thymus
21	chr6:167383200-167385000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:167383200-167385200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:167383200-167396200	Weak transcription	Fetal Brain Female	brain
24	chr6:167383200-167411200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:167383400-167386200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr6:167383400-167386600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr6:167383400-167387200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr6:167383400-167389800	Weak transcription	K562	blood
29	chr6:167383400-167411000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:167383600-167384800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:167383600-167385400	Enhancers	Primary T cells from cord blood	blood
32	chr6:167383600-167385600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:167383600-167391000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:167383800-167384800	Enhancers	Primary B cells from cord blood	blood
35	chr6:167383800-167385400	Enhancers	Primary hematopoietic stem cells	blood
36	chr6:167383800-167385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:167383800-167392000	Weak transcription	Brain Germinal Matrix	brain
38	chr6:167384000-167384800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:167384000-167396200	Weak transcription	GM12878-XiMat	blood
40	chr6:167384000-167410600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:167384000-167411000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:167384000-167411000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:167384200-167385000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:167384200-167385000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:167384200-167385000	Strong transcription	Fetal Intestine Small	intestine
46	chr6:167384400-167385400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:167384400-167385600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:167384400-167385800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:167384400-167386200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr6:167384400-167401400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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